Routine testing for inherited and acquired thrombophilia defects is frequently performed in pediatric patients with thromboembolic events (TEEs). No consensus guidelines exist regarding the timing of testing or the type of patients to be tested. The primary objective of our study, therefore, was to determine whether thrombophilia testing during the acute TEE setting affected clinical management in pediatric patients. A secondary aim included estimation of potential harm from thrombophilia testing. We retrospectively reviewed data on all pediatric patients diagnosed with a TEE during a 1-year period. Fifty-two (51%) of 102 patients with a TEE underwent thrombophilia testing during the acute phase, with 26 patients (50%) having a positive test result during the acute phase. Only 12% of patients tested were confirmed to have a thrombophilia eventually, yielding a false-positive rate of ∼7% for testing when performed in the acute setting. There were no changes to the acute management, regardless of a positive or negative result. Testing resulted in unnecessary blood loss in 12 patients younger than 1 year and acute testing cost approximately $82 000. Our data show that thrombophilia testing during acute TEEs in pediatric patients did not impact clinical management. There is also a potential for false-positive tests leading to unnecessary long-term anticoagulation. These findings suggest against thrombophilia testing during acute TEE setting in children.